From: Peter Freddolino (
Date: Mon Apr 14 2008 - 10:26:40 CDT

Hi Jorgen,
the internal coordinate entries only come into play if there are missing
atoms when you run psfgen. Are there any missing atoms in your input
pdb? And are the amino acids of interest already in the D form at that

Jorgen Simonsen wrote:
> Hi,
> I am trying to generate a topology file for a protein which contains
> some D-amino acids - I change the topology file as according to the
> tutorial but when I look at the amino acids they are still in the
> L-conformation as if the internal coordinates of the topology file has
> not been read?
> Is there a way to force the topology file to read the IC when creating
> PDB and PSF ?
> Best
> Jorgen